BN1814 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 1.4315e-08 2.3131e-04
Layer 2 3.2055e-07 6.6155e-03
Layer 3 5.4208e-07 4.4837e-04
Layer 4 2.1297e-06 8.9275e-05
WM 9.7121e-01 7.1866e-01
Layer 1 9.7963e-01 4.8465e-01
Layer 6 9.9997e-01 2.2395e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
STRAP Expression Distribution
Gene Specificity Score (GSS)
STRAP GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
STRAP Layer 4 2.2900 0.6841
RNPS1 Layer 4 2.1367 0.6833
HPCA Layer 4 2.6191 0.6818
RUFY3 Layer 3 2.0859 0.6813
PTPA Layer 4 2.3281 0.6796
SYNGR3 Layer 5 2.5000 0.6779
FGF12 Layer 4 2.4697 0.6772
VDAC3 Layer 4 2.2949 0.6763
TMEM14A Layer 5 2.1348 0.6752
SF3B2 Layer 4 2.2051 0.6737
SNCA Layer 5 2.2266 0.6723
DDB1 Layer 5 2.2969 0.6723
KHDRBS3 Layer 4 2.4785 0.6715
MDH2 Layer 5 2.1875 0.6705
SQSTM1 Layer 5 2.0957 0.6693
WDR47 Layer 4 2.2773 0.6683
BNIP3 Layer 4 2.3398 0.6679
ARL8A Layer 5 2.1152 0.6678
MRPS21 Layer 5 2.1543 0.6662
SATB1 Layer 4 2.6367 0.6658
ELAVL4 Layer 4 2.5332 0.6658
TSC22D3 Layer 5 2.3125 0.6636
MBNL2 Layer 4 2.0889 0.6629
NISCH Layer 4 2.1416 0.6628
SLC2A3 Layer 5 2.3926 0.6626
ATP5PB Layer 5 2.0820 0.6624
CLTA Layer 5 2.1484 0.6618
MAPK8IP3 Layer 4 2.3086 0.6616
KIFAP3 Layer 4 2.3057 0.6615
POLR2E Layer 4 2.2578 0.6614
OTUB1 Layer 5 2.4238 0.6613
RIMS3 Layer 3 2.2871 0.6609
SULT4A1 Layer 5 2.3711 0.6606
ADAR Layer 3 2.1387 0.6602
SYNGR1 Layer 4 2.2070 0.6596
ARHGDIG Layer 5 2.2129 0.6595
INPP5F Layer 3 2.1387 0.6594
WAC Layer 4 2.3125 0.6591
DGKZ Layer 4 2.1914 0.6591
MYO5A Layer 5 2.3125 0.6590
AMZ2 Layer 4 2.1514 0.6589
CPLX1 Layer 5 2.3711 0.6587
SLC25A3 Layer 5 2.0820 0.6581
PRRT1 Layer 5 2.2266 0.6577
CALY Layer 3 2.1055 0.6572
AGAP3 Layer 3 2.0625 0.6571
OPCML Layer 5 2.2715 0.6565
CEND1 Layer 5 2.2578 0.6561
CAMK2G Layer 4 2.3965 0.6560
AP3S1 Layer 5 2.1094 0.6554

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1814
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1814_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1814/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1814/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1814/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1814/report/PD/BN1814_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1814/report/PD/BN1814_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:40:52
  • Number of Processes: 10
  • Spending Time: 0h 3m